Table 3.
Association results for the replication cohort (Germany+Texas+Utah) *
| Marker | chr | kbp | locus | MA | Germany +Texas +Utah |
|||||
|---|---|---|---|---|---|---|---|---|---|---|
| MAF |
Joint Analysis |
Meta Analysis |
||||||||
| JIA | Control | P-value§ | OR [95%CI] | P-value | OR [95%CI] | |||||
| Intracellular signaling | ||||||||||
| rs6679677 | 1 | 114105 | PTPN22 | A | 0.151 | 0.102 | 1.24 × 10−6 | 1.53 [1.29–1.82] | 4.19 × 10−6 | 1.52 [1.27–1.83] |
| rs2476601† | 1 | 114179 | PTPN22 | A | 0.149 | 0.095 | 9.07 × 10−8 | 1.64 [1.37–1.97] | 3.12 × 10−7 | 1.63 [1.35–1.97] |
| rs2488457 | 1 | 114216 | PTPN22 | C | 0.252 | 0.204 | 1.96 × 10−4 | 1.31 [1.13–1.50] | 3.07 × 10−4 | 1.30 [1.12–1.51] |
| rs2542151 | 18 | 12770 | PTPN2 | G | 0.180 | 0.174 | 1.62 × 10−1 | 0.67 [0.38–1.18] | 2.48 × 10−1 | 0.43 [0.17–1.09] |
| rs2847297 | 18 | 12787 | PTPN2 | G | 0.358 | 0.349 | 4.99 × 10−1 | 1.04 [0.92–1.18] | 5.79 × 10−1 | 1.02 [0.90–1.17] |
| rs1893217† | 18 | 12799 | PTPN2 | C | 0.191 | 0.161 | 8.87 × 10−3 | 1.24 [1.05–1.45] | 7.93 × 10−3 | 1.20 [1.01–1.41] |
| rs7234029 | 18 | 12867 | PTPN2 | C | 0.183 | 0.158 | 2.90 × 10−2 | 1.19 [1.02–1.39] | 6.39 × 10−2 | 1.15 [0.97–1.35] |
| Cytokines and cytokine receptors | ||||||||||
| rs11465804† | 1 | 67475 | IL23R | G | 0.064 | 0.062 | 7.96 × 10−1 | 1.03 [0.81–1.32] | 7.02 × 10−1 | 1.01 [0.79–1.30] |
| rs2104286 | 10 | 6139 | IL2RA | C | 0.258 | 0.266 | 5.33 × 10−1 | 0.96 [0.84–1.10] | 8.45 × 10−1 | 0.99 [0.86–1.14] |
| rs17388568 | 4 | 123549 | ADAD1-IL2-IL21 | A | 0.342 | 0.292 | 5.54 × 10−4 | 1.25 [1.10–1.41] | 2.02 × 10−3 | 1.21 [1.06–1.38] |
| rs13143866 | 4 | 123760 | ADAD1-IL2-IL21 | T | 0.227 | 0.271 | 6.45 × 10−4 | 0.79 [0.69–0.90] | 6.09 × 10−3 | 0.83 [0.72–0.96] |
| Transcriptional regulators | ||||||||||
| rs3821236 | 2 | 191611 | STAT4 | A | 0.241 | 0.203 | 2.42 × 10−3 | 1.25 [1.08–1.44] | 1.24 × 10−3 | 1.26 [1.08–1.46] |
| rs7574865† | 2 | 191673 | STAT4 | T | 0.275 | 0.221 | 4.14 × 10−5 | 1.33 [1.16–1.53] | 4.75 × 10−5 | 1.31 [1.14–1.51] |
| rs7746082 | 6 | 106542 | BLIMP1 | C | 0.291 | 0.288 | 8.17 × 10−1 | 1.02 [0.89–1.16] | 6.81 × 10−1 | 1.00 [0.88–1.15] |
| Unknown | ||||||||||
| rs17696736 | 12 | 110971 | C12orf30 | G | 0.478 | 0.428 | 9.52 × 10−4 | 1.22 [1.08–1.37] | 1.90 × 10−3 | 1.19 [1.06–1.35] |
| rs7151781 | 14 | 42557 | Intergenic | C | 0.361 | 0.351 | 4.83 × 10−1 | 1.05 [0.92–1.18] | 5.08 × 10−1 | 1.02 [0.90–1.17] |
| Other | ||||||||||
| rs1010824 | 8 | 108321 | ANGPT1 | T | 0.155 | 0.178 | 4.21 × 10−2 | 0.85 [0.72–0.99] | 2.37 × 10−2 | 0.83 [0.70–0.98] |
| rs1132200 | 3 | 120634 | TMEM39A | T | 0.148 | 0.161 | 2.19 × 10−1 | 0.90 [0.77–1.06] | 1.75 × 10−1 | 0.86 [0.73–1.02] |
| rs10259085† | 7 | 7235 | C1GALT1/COL28A1 | T | 0.450 | 0.468 | 2.33 × 10−1 | 0.93 [0.82–1.05] | 1.33 × 10−1 | 0.90 [0.79–1.02] |
| rs7993214† | 13 | 39249 | COG6 | T | 0.311 | 0.359 | 8.29 × 10−4 | 0.80 [0.71–0.91] | 1.92 × 10−3 | 0.81 [0.71–0.93] |
*
For the “Replication cohort, the association findings of individual sample collections (Texas, Utah, Germany) are not shown, but rather combined in “joint” and “meta”-analyses All SNPs passed HWE testing
†
Genotypes were imputed in the initial cohort
§
The additive genetic model was used for all SNPs except rs2542151; recessive model used for both Joint and Meta analyses